From 747b951ca1541460618b272d8aa9e81bf2cfd275 Mon Sep 17 00:00:00 2001 From: nisse3000 Date: Fri, 20 Apr 2018 16:26:07 -0700 Subject: [PATCH] Adaptions to new pymatgen version and requireing most recent pymatgen versioin. --- emmet/materials/site_descriptors.py | 10 +------- .../materials/tests/test_site_descriptors.py | 24 +++++++++---------- requirements.txt | 2 +- setup.py | 2 +- 4 files changed, 15 insertions(+), 23 deletions(-) diff --git a/emmet/materials/site_descriptors.py b/emmet/materials/site_descriptors.py index 5e8c7f79cd..06eda02834 100644 --- a/emmet/materials/site_descriptors.py +++ b/emmet/materials/site_descriptors.py @@ -15,12 +15,6 @@ __author__ = "Nils E. R. Zimmermann " -cls_to_abbrev = { - 'OPSiteFingerprint': 'opsf', 'CrystalSiteFingerprint': 'csf', \ - 'VoronoiNN': 'vnn', 'JMolNN': 'jmnn', 'MinimumDistanceNN': 'mdnn', \ - 'MinimumOKeeffeNN': 'moknn', 'MinimumVIRENN': 'mvirenn', \ - 'BrunnerNN': 'bnn'} - class SiteDescriptorsBuilder(Builder): def __init__(self, materials, site_descriptors, mat_query=None, **kwargs): @@ -48,9 +42,7 @@ def __init__(self, materials, site_descriptors, mat_query=None, **kwargs): self.sds = {} for nn in NearNeighbors.__subclasses__(): nn_ = getattr(pymatgen.analysis.local_env, nn.__name__) - t = nn.__name__ if nn.__name__ \ - not in cls_to_abbrev.keys() \ - else cls_to_abbrev[nn.__name__] + t = nn.__name__ k = 'cn_{}'.format(t) self.sds[k] = CoordinationNumber(nn_(), use_weights='none') k = 'cn_wt_{}'.format(t) diff --git a/emmet/materials/tests/test_site_descriptors.py b/emmet/materials/tests/test_site_descriptors.py index a457529d5c..02d52c8d3c 100644 --- a/emmet/materials/tests/test_site_descriptors.py +++ b/emmet/materials/tests/test_site_descriptors.py @@ -57,18 +57,18 @@ def test_get_all_site_descriptors(self): d = sd_builder.get_site_descriptors_from_struct(Structure.from_dict(C["structure"])) for di in d.values(): self.assertEqual(len(di), 2) - self.assertEqual(d['cn_vnn'][0]['CN_VoronoiNN'], 20) - self.assertAlmostEqual(d['cn_wt_vnn'][0]['CN_VoronoiNN'], 4.5381162) - self.assertEqual(d['cn_jmnn'][0]['CN_JMolNN'], 4) - self.assertAlmostEqual(d['cn_wt_jmnn'][0]['CN_JMolNN'], 4.9617398) - self.assertEqual(d['cn_mdnn'][0]['CN_MinimumDistanceNN'], 4) - self.assertAlmostEqual(d['cn_wt_mdnn'][0]['CN_MinimumDistanceNN'], 4) - self.assertEqual(d['cn_moknn'][0]['CN_MinimumOKeeffeNN'], 4) - self.assertAlmostEqual(d['cn_wt_moknn'][0]['CN_MinimumOKeeffeNN'], 4) - self.assertEqual(d['cn_mvirenn'][0]['CN_MinimumVIRENN'], 4) - self.assertAlmostEqual(d['cn_wt_mvirenn'][0]['CN_MinimumVIRENN'], 4) - self.assertEqual(d['cn_bnn'][0]['CN_BrunnerNN'], 4) - self.assertAlmostEqual(d['cn_wt_bnn'][0]['CN_BrunnerNN'], 4) + self.assertEqual(d['cn_VoronoiNN'][0]['CN_VoronoiNN'], 20) + self.assertAlmostEqual(d['cn_wt_VoronoiNN'][0]['CN_VoronoiNN'], 4.5381162) + self.assertEqual(d['cn_JMolNN'][0]['CN_JMolNN'], 4) + self.assertAlmostEqual(d['cn_wt_JMolNN'][0]['CN_JMolNN'], 4.9617398) + self.assertEqual(d['cn_MinimumDistanceNN'][0]['CN_MinimumDistanceNN'], 4) + self.assertAlmostEqual(d['cn_wt_MinimumDistanceNN'][0]['CN_MinimumDistanceNN'], 4) + self.assertEqual(d['cn_MinimumOKeeffeNN'][0]['CN_MinimumOKeeffeNN'], 4) + self.assertAlmostEqual(d['cn_wt_MinimumOKeeffeNN'][0]['CN_MinimumOKeeffeNN'], 4) + self.assertEqual(d['cn_MinimumVIRENN'][0]['CN_MinimumVIRENN'], 4) + self.assertAlmostEqual(d['cn_wt_MinimumVIRENN'][0]['CN_MinimumVIRENN'], 4) + self.assertEqual(d['cn_BrunnerNN_reciprocal'][0]['CN_BrunnerNN_reciprocal'], 4) + self.assertAlmostEqual(d['cn_wt_BrunnerNN_reciprocal'][0]['CN_BrunnerNN_reciprocal'], 4) self.assertAlmostEqual(d['opsf'][0]['tetrahedral CN_4'], 0.9995) #self.assertAlmostEqual(d['csf'][0]['tetrahedral CN_4'], 0.9886777) ds = sd_builder.get_statistics(d) diff --git a/requirements.txt b/requirements.txt index ffef99be9f..9d155fe5f0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ atomate>=0.6.5 -pymatgen>=2018.4.6 +pymatgen>=2018.4.20 monty>=1.0.1 pydash==4.1.0 unittest2==1.1.0 diff --git a/setup.py b/setup.py index 993cd2bd0f..360464490d 100644 --- a/setup.py +++ b/setup.py @@ -20,7 +20,7 @@ package_data={}, zip_safe=False, install_requires=[ - 'atomate', 'pymatgen>=2018.3.2','maggma','monty', + 'atomate', 'pymatgen>=2018.4.20','maggma','monty', 'six', 'pydash', 'tqdm', 'matminer', 'prettyplotlib', "pybtex" ],